BMRBj - BMREntryMaster

Found 1 Document (0.372 seconds)

BMRB: 36345

7BWI

Solution structure of recombinant APETx1

Authors

Matsumura, K., Kobayashi, N., Kurita, J., Nishimura, Y., Yokogawa, M., Imai, S., Shimada, I., Osawa, M.

Assembly

Kappa-actitoxin-Ael2a

Entity

1. Kappa-actitoxin-Ael2a (polymer, Thiol state: all disulfide bound), 42 monomers, 4558.200 Da Detail

GTTCYCGKTI GIYWFGTKTC PSNRGYTGSC GYFLGICCYP VD

Formula weight

4558.2 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS37:SG
2	disulfide	sing	1:CYS6:SG	1:CYS30:SG
3	disulfide	sing	1:CYS20:SG	1:CYS38:SG

Source organism

Anthopleura elegantissima

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.3 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.3 % (454 of 462)	99.1 % (232 of 234)	97.8 % (181 of 185)	95.3 % (41 of 43)
Backbone	96.8 % (240 of 248)	97.8 % (88 of 90)	96.6 % (114 of 118)	95.0 % (38 of 40)
Sidechain	100.0 % (248 of 248)	100.0 % (144 of 144)	100.0 % (101 of 101)	100.0 % (3 of 3)
Aromatic	100.0 % (72 of 72)	100.0 % (36 of 36)	100.0 % (35 of 35)	100.0 % (1 of 1)
Methyl	100.0 % (32 of 32)	100.0 % (16 of 16)	100.0 % (16 of 16)

1. Kappa-actitoxin-Ael2a

GTTCYCGKTI GIYWFGTKTC PSNRGYTGSC GYFLGICCYP VD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.691 mM [U-100% 13C; U-100% 15N] APETx1, 20 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 7BWI, Strand ID: A Detail

Release date

2020-09-08

Citation

Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization
Matsumura, K., Shimomura, T., Kubo, Y., Kobayashi, N., Imai, S., Yanase, N., Akimoto, M., Yokogawa, M., Ikeda, I., Kurita, J., Nishimura, Y., Shimada, I., Osawa, M.
BMC Mol. Cell Biol. (2021), 22, 3-3, PubMed 33413079 , DOI 10.1186/s12860-020-00337-3 , Abstract

Related entities 1. Kappa-actitoxin-Ael2a, : 1 : 2 : 2 : 23 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.691 mM [U-100% 13C; U-100% 15N] APETx1, 20 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III HD - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III HD - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

4 3D HNCACB

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

6 3D HNCO

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

7 3D HCCH-COSY

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

9 3D 1H-15N NOESY

Instrument

Bruker AVANCE III HD - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE III HD - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE III HD - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

12 3D 1H-15N TOCSY

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

14 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

15 3D 1H-15N NOESY

Instrument

Bruker Avance 600 - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	APETx1	[U-100% 13C; U-100% 15N]	protein	0.691 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr36345_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:4:CYS:SG	1:37:CYS:SG	oxidized, CA 53.712, CB 45.178 ppm	oxidized, CA 54.012, CB 43.683 ppm	n/a
1:6:CYS:SG	1:30:CYS:SG	oxidized, CA 52.141, CB 39.229 ppm	oxidized, CA 55.739, CB 43.246 ppm	n/a
1:20:CYS:SG	1:38:CYS:SG	oxidized, CA 55.361, CB 41.639 ppm	oxidized, CA 56.164, CB 45.573 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr36345_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	483		100.0 (chain: 1, length: 42)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 42, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 263
  - ¹³C chemical shifts: 180
  - ¹⁵N chemical shifts: 40
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	234	231	98.7
¹³C chemical shifts	185	180	97.3
¹⁵N chemical shifts	43	40	93.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	87	96.7
¹³C chemical shifts	84	79	94.0
¹⁵N chemical shifts	40	37	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	144	144	100.0
¹³C chemical shifts	101	101	100.0
¹⁵N chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0
¹³C chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	36	100.0
¹³C chemical shifts	35	35	100.0
¹⁵N chemical shifts	1	1	100.0

Keywords TOXIN

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Found 1 Document (0.372 seconds)

BMRB: 36345

Sample

Related entities 1. Kappa-actitoxin-Ael2a, : 1 : 2 : 2 : 23 entities Detail

Experiments performed 15 experiments Detail

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Chemical shift validation 3 contents Detail